Alignments for a candidate for ytfR in Collimonas pratensis Ter91

GapMind for catabolism of small carbon sources

Alignments for a candidate for ytfR in Collimonas pratensis Ter91

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate WP_061941304.1 CPter91_RS14020 sugar ABC transporter ATP-binding protein

Query= ecocyc::YTFR-MONOMER
         (500 letters)



>NCBI__GCF_001584185.1:WP_061941304.1
          Length = 519

 Score =  481 bits (1238), Expect = e-140
 Identities = 253/496 (51%), Positives = 337/496 (67%), Gaps = 6/496 (1%)

Query: 10  LRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLE 69
           L   G+ K F GV AL+ V   L  GE+  L+G+NGAGKSTLIK LTGVY  D G I L 
Sbjct: 20  LTLSGICKAFGGVTALNEVALRLYPGEVHTLMGQNGAGKSTLIKVLTGVYTPDSGRILLH 79

Query: 70  GQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATEL 129
           GQ + P++T  AQ LGI TVYQEVNL PN+SVA+N+FIGR PK++G +  K M+++A +L
Sbjct: 80  GQPVQPRSTLEAQSLGISTVYQEVNLCPNLSVAENIFIGRYPKKYGAIDWKSMQQQAQQL 139

Query: 130 MASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMR 189
           +      +DV  PL+R+ +A+QQ+VAI RA+ +SAKVLILDEPT+SLD  EV+LLF+++R
Sbjct: 140 LHELHVRIDVAAPLSRYPLAIQQMVAISRALSISAKVLILDEPTSSLDDAEVKLLFEVLR 199

Query: 190 QLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRE---- 245
           +LR +G++++FVTHFL+Q Y++SDRITVLRNG   G     +L +++LV  M+G +    
Sbjct: 200 KLRAQGMAILFVTHFLEQTYEISDRITVLRNGQLEGEYLASQLSRLDLVNKMVGSQTSSS 259

Query: 246 --LDTHALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETA 303
             LD    +   +       V   +  G+ G +AP DL++R GE++GL GLLGSGRTETA
Sbjct: 260 PNLDAADGRAEPQVDSGQTAVLQARGLGRNGILAPLDLDLRGGEVLGLCGLLGSGRTETA 319

Query: 304 EVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILAL 363
            ++FG    DSGT  IKGK +   SP  A   GIGFC EDRK +G I   SVRENI+LAL
Sbjct: 320 RLLFGADKPDSGTLQIKGKVEKFHSPRDAIAAGIGFCSEDRKKEGAILELSVRENIVLAL 379

Query: 364 QAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQF 423
           QA+ G LR I R+ QQ +A  +++ LGI+T   E PI  LSGGNQQK LL+RWL T P  
Sbjct: 380 QARAGLLRVIPRRRQQALASDYVKWLGIKTADIETPIGSLSGGNQQKALLARWLATDPAM 439

Query: 424 LILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAE 483
           LILDEPTRGIDV A  EI+  +  LC  G+A+L ISSE+ E++  +DR++++RDRK   E
Sbjct: 440 LILDEPTRGIDVRAKQEIMEHVIALCRKGMAILFISSEISEVLRVSDRMLVLRDRKACGE 499

Query: 484 IPLAELSVPAIMNAIA 499
               EL   +++  IA
Sbjct: 500 YLRGELDEDSVLQVIA 515



 Score = 83.6 bits (205), Expect = 2e-20
 Identities = 64/242 (26%), Positives = 123/242 (50%), Gaps = 12/242 (4%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68
           +L+  GL +   G+ A   +D  LR GE++ L G  G+G++   + L G    D GT+ +
Sbjct: 280 VLQARGLGR--NGILA--PLDLDLRGGEVLGLCGLLGSGRTETARLLFGADKPDSGTLQI 335

Query: 69  EGQAISPKNTAHAQQLGIGTVYQE---VNLLPNMSVADNLFIGREPKRFGLLR---RKEM 122
           +G+     +   A   GIG   ++      +  +SV +N+ +  +  R GLLR   R+  
Sbjct: 336 KGKVEKFHSPRDAIAAGIGFCSEDRKKEGAILELSVRENIVLALQA-RAGLLRVIPRRRQ 394

Query: 123 EKRATELMASYGF-SLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEV 181
           +  A++ +   G  + D+  P+   S   QQ   + R +     +LILDEPT  +D +  
Sbjct: 395 QALASDYVKWLGIKTADIETPIGSLSGGNQQKALLARWLATDPAMLILDEPTRGIDVRAK 454

Query: 182 ELLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMM 241
           + + + +  L  +G++++F++  + +V +VSDR+ VLR+    G     EL +  +++++
Sbjct: 455 QEIMEHVIALCRKGMAILFISSEISEVLRVSDRMLVLRDRKACGEYLRGELDEDSVLQVI 514

Query: 242 LG 243
            G
Sbjct: 515 AG 516


Lambda     K      H
   0.321    0.138    0.391 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 630
Number of extensions: 25
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 500
Length of database: 519
Length adjustment: 34
Effective length of query: 466
Effective length of database: 485
Effective search space:   226010
Effective search space used:   226010
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources